I did encode a DCP with burnt-in subtitles.
Later reopened the project and deactivated the subtitles completely, to create a clean DCP. Launching the encoding did not see the change and very efficiently copies the previously created video, still with the burnt-in subtitles.
I expected some optimisation as only the parts with removed subtitles need to be reencoded, in a similar way that it happens the other way round, when adding subtitles.